From temesgen.dadi@fu-berlin.de Tue Mar 08 21:59:39 2016 Received: from outpost9.zedat.fu-berlin.de ([130.133.4.95]) by list1.zedat.fu-berlin.de (Exim 4.85) for seqan-dev@lists.fu-berlin.de with esmtps (TLSv1.2:DHE-RSA-AES256-GCM-SHA384:256) (envelope-from ) id <1adOjC-0009oL-71>; Tue, 08 Mar 2016 21:59:38 +0100 Received: from relay2.zedat.fu-berlin.de ([130.133.4.80]) by outpost.zedat.fu-berlin.de (Exim 4.85) for seqan-dev@lists.fu-berlin.de with esmtps (TLSv1.2:DHE-RSA-AES256-GCM-SHA384:256) (envelope-from ) id <1adOjC-001Opz-1p>; Tue, 08 Mar 2016 21:59:38 +0100 Received: from cas3.campus.fu-berlin.de ([130.133.170.203]) by relay2.zedat.fu-berlin.de (Exim 4.85) for seqan-dev@lists.fu-berlin.de with esmtps (TLSv1:AES256-SHA:256) (envelope-from ) id <1adOjB-0031Z6-O7>; Tue, 08 Mar 2016 21:59:37 +0100 Received: from EX01B.campus.fu-berlin.de ([130.133.170.131]) by CAS3.campus.fu-berlin.de ([130.133.170.203]) with mapi id 14.03.0279.002; Tue, 8 Mar 2016 21:59:36 +0100 From: "Dadi, Temesgen Hailemariam" To: SeqAn Development Thread-Topic: [Seqan-dev] problem in LoadReads Thread-Index: AQHRbVsijJ7WfTw5JUiTV4U8pf3JIJ8325mAgBgviAA= Message-ID: <7DB8383C-5840-4013-A309-56735F3B98EF@fu-berlin.de> References: <3275efa85bb114a748d59692074cd89f.squirrel@mail.mpi-inf.mpg.de> <1960016.BlySc0OUpc@celegans.imp.fu-berlin.de> In-Reply-To: <1960016.BlySc0OUpc@celegans.imp.fu-berlin.de> Accept-Language: en-US, de-DE Content-Language: en-US X-MS-Has-Attach: yes X-MS-TNEF-Correlator: Content-Type: multipart/signed; boundary="Apple-Mail=_78F56071-3223-44E3-963D-E0C1F2F040D7"; protocol="application/pkcs7-signature"; micalg=sha1 MIME-Version: 1.0 Date: Tue, 08 Mar 2016 21:59:35 +0100 X-Original-Date: Tue, 8 Mar 2016 20:59:35 +0000 X-Originating-IP: 130.133.170.203 X-Original-X-Originating-IP: [130.133.170.191] X-ZEDAT-Hint: XA X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1457470778-00052D45-46C2F6A7/0/0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.000000, version=1.2.4 X-Spam-Flag: NO X-Spam-Status: No, score=-50.0 required=5.0 tests=ALL_TRUSTED,HTML_MESSAGE, RP_MATCHES_RCVD X-Spam-Checker-Version: SpamAssassin 3.4.1 on Palau.ZEDAT.FU-Berlin.DE X-Spam-Level: Subject: Re: [Seqan-dev] problem in LoadReads X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.16 Precedence: list Reply-To: SeqAn Development List-Id: SeqAn Development List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Tue, 08 Mar 2016 20:59:39 -0000 --Apple-Mail=_78F56071-3223-44E3-963D-E0C1F2F040D7 Content-Type: multipart/alternative; boundary="Apple-Mail=_3D860875-6117-46FD-9F74-115552E6811C" --Apple-Mail=_3D860875-6117-46FD-9F74-115552E6811C Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=utf-8 I tried to reproduce your bug with the following simple code fragment: FragmentStore<> store; =20 CharString fileNameR =3D = =E2=80=9C~/workspace/example/reads_pe_N6000.GA.R.fastq"; CharString fileNameL =3D = =E2=80=9C~/workspace/example/reads_pe_N6000.CT.L.fastq"; =20 loadReads(store, fileNameR, fileNameR); and I couldn=E2=80=99t. All the reads were loaded correctly.=20 Can you please provide me with a code fragment that can produce the = problem?=20 Thanks! Temesgen H. Dadi PhD Candidate (IMPRS-CBSC, JSMC) Skype ID: temeehi Freie Universit=C3=A4t Berlin Institut f=C3=BCr Informatik | Institut f=C3=BCr = Mikrobiologie AG Algorithmische Bioinformatik | und = Tierseuche Takustra=C3=9Fe 9, 14195 Berlin, Germany | = Robert-von-Ostertag-Str. 7-13 Telephone: +49 (0)30 838-75246 | Geb=C3=A4ude 35, 14163 = Berlin, Germany > On 22 Feb 2016, at 12:24, Hannes Hauswedell = wrote: >=20 > Am Montag, 22. Februar 2016, 11:23:23 schrieb Luis Enrique Ramirez = Chavez: >> Hi Seqan Devs, >>=20 >> I am currently working a project that used Seqan 1.4 and now I am = updating >> to Seqan 2.1. I think that maybe I have found a bug in Seqan. The = problem >> is that LoadReads from FragmentStore is not returning the same as in = the >> previous version for the same call, I did a little research = comparing >> both versions. >=20 > Thanks for your bug report and research! >=20 >> The code of loadReads have change from one version to the other, in = both >> versions it's defined in seqan/store/store_io.h at line 1159 for old >> version and at line 1273 for the new version but the behave is = different >> and I think here is the problem. >>=20 >> in old version there is this part: >>=20 >> MultiSeqFile multiSeqFileL, multiSeqFileR; >> if (!open(multiSeqFileL.concat, toCString(fileNameL), OPEN_RDONLY)) >> return false; >> if (!open(multiSeqFileR.concat, toCString(fileNameR), OPEN_RDONLY)) >> return false; >=20 > This looks like the file is from a previous save() so it is in SeqAn = binary=20 > format. >=20 >=20 >> The flow is working correctly and the ifs don't reach the return = false but >> in the new version the code is like this >>=20 >> SeqFileIn seqFileL, seqFileR; >> if (!open(seqFileL, toCString(fileNameL)) || !open(seqFileR, >> toCString(fileNameR))) >> return false; >=20 > This looks like it is trying to load it as a regular sequence file so = this=20 > seems something different from above. You might be right, that this is = the=20 > place! >=20 >> here the execution always always return false. I inspected and its = because >> a different open function its called and here is where I think is the >> bug. >>=20 >> In seqan 1.4 the open function called is from string_map defined in >> /include/seqan/file/string_mmap.h however in 2.x the open function = that is >> being called is from /include/seqan/stream/formatted_file.h. The open = from >> string_mmap.h exists in 2.x and I think is the function that wanted = to be >> called. LoadReads calls open with SeqFileIn in the new version while = in >> previous with MultiSeqFile but MultiSeqFile is not available in new >> version >>=20 >> Can you please check if that is a bug >=20 > I have created an issue in the bugtracker that you can follow: > https://github.com/seqan/seqan/issues/1484 >=20 > Best regards, > Hannes > --=20 > Hannes Hauswedell >=20 > PhD student > Max Planck Institute for Molecular Genetics / Freie Universit=C3=A4t = Berlin >=20 > address Institut f=C3=BCr Informatik > Takustra=C3=9Fe 9 > Room 019 > 14195 Berlin > telephone +49 (0)30 838-75241 > fax +49 (0)30 838-75218 > e-mail hannes.hauswedell@[molgen.mpg.de|fu-berlin.de] >=20 > _______________________________________________ > seqan-dev mailing list > seqan-dev@lists.fu-berlin.de > https://lists.fu-berlin.de/listinfo/seqan-dev --Apple-Mail=_3D860875-6117-46FD-9F74-115552E6811C Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=utf-8 I tried to reproduce your bug with the following simple code = fragment:

    FragmentStore<> store;

    

    = CharString fileNameR =3D = =E2=80=9C~/workspace/example/reads_pe_N6000.GA.R.fastq";
    CharString fileNameL =3D = =E2=80=9C~/workspace/example/reads_pe_N6000.CT.L.fastq";

    

    loadReads(store, = fileNameR, fileNameR);

and I couldn=E2=80=99= t. All the reads were loaded correctly. 

Can you = please provide me with a code fragment that can produce the = problem? 

Thanks!

Temesgen H. = Dadi
PhD Candidate (IMPRS-CBSC, JSMC)
Skype ID: = temeehi
Freie Universit=C3=A4t = Berlin
Institut f=C3=BCr Informatik =                 |     =      Institut f=C3=BCr Mikrobiologie
AG = Algorithmische Bioinformatik         |     =                  und = Tierseuche
Takustra=C3=9Fe 9, 14195 Berlin, = Germany     |       Robert-von-Ostertag-Str. = 7-13
Telephone: +49 (0)30 838-75246         =  |   Geb=C3=A4ude 35, 14163 Berlin, Germany





On 22 Feb 2016, at 12:24, Hannes Hauswedell <hannes.hauswedell@fu-berlin.de> wrote:

Am = Montag, 22. Februar 2016, 11:23:23 schrieb Luis Enrique Ramirez = Chavez:
Hi Seqan = Devs,

I am currently working a project that = used Seqan 1.4 and now I am updating
to Seqan 2.1. I think = that maybe I have found a bug in Seqan. The problem
is = that LoadReads from FragmentStore is not returning the same as in the
previous version for the same call, I did a little research =  comparing
both versions.

Thanks for your bug report and = research!

The code of loadReads  have change from one version to = the other, in both
versions it's defined in = seqan/store/store_io.h at line 1159 for old
version and at = line 1273 for the new version but the behave is different
and I think here is the problem.

in old version there is this part:

MultiSeqFile multiSeqFileL, multiSeqFileR;
if = (!open(multiSeqFileL.concat, toCString(fileNameL), OPEN_RDONLY))
 return false;
if = (!open(multiSeqFileR.concat, toCString(fileNameR), OPEN_RDONLY))
 return false;

This looks like the file is from a previous save() so it is = in SeqAn binary
format.


The flow is working = correctly and the ifs don't reach the return false but
in = the new version the code is like this

SeqFileIn seqFileL, seqFileR;
if = (!open(seqFileL, toCString(fileNameL)) || !open(seqFileR,
toCString(fileNameR)))
  return = false;

This looks like it is = trying to load it as a regular sequence file so this
seems = something different from above. You might be right, that this is the
place!

here the execution always always return false. I inspected = and its because
a different open function its called and = here is where I think is the
bug.

In seqan 1.4 the open function called is from =  string_map defined in
/include/seqan/file/string_mmap.h however in 2.x the open = function that is
being called is from = /include/seqan/stream/formatted_file.h. The open from
string_mmap.h exists in 2.x and I think is the function that = wanted to be
called. LoadReads calls open with SeqFileIn = in the new version while in
previous with MultiSeqFile but = MultiSeqFile is not available in new
version

Can you please check if that is a bug

I have created an issue in the = bugtracker that you can follow:
https://github.com/seqan/seqan/issues/1484

Best regards,
Hannes
--
Hannes Hauswedell

PhD student
Max Planck Institute for Molecular = Genetics / Freie Universit=C3=A4t Berlin

address     Institut f=C3=BCr = Informatik
=            Takustra= =C3=9Fe 9
=            Room = 019
=            14195 = Berlin
telephone   +49 (0)30 838-75241
fax         +49 (0)30 = 838-75218
e-mail =      hannes.hauswedell@[molgen.mpg.de|fu-berlin.d= e]

_______________________________________________
seqan-dev mailing list
seqan-dev@lists.fu-berlin.de
https://lists.fu-berlin.de/listinfo/seqan-dev

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S2zl/HPhWVMASbkuAcIQppP51B7j8vvglvFGJ3h3Nf1Ur7GmmHopoIvBQbvULmBVNHUCd+bL8roj WIWSONafaQcQi9e0GUPZ76KeOyJeqLBbFr279NwxPydSdnHY04XZnaENeeBPHDRSpks/ENqcp40T 0ixD4ByhSjSNxqbG3niu72YcVrrPPhwz7Ky9/6NGsgVaeon479kzDqiTz8n5G5dqI+BESDc893k0 nNeFXWti1m99X6gDFoAumpHiwczFpMIAAAAAAAA= --Apple-Mail=_78F56071-3223-44E3-963D-E0C1F2F040D7-- From lramirez@mpi-inf.mpg.de Thu Mar 10 18:26:09 2016 Received: from relay1.zedat.fu-berlin.de ([130.133.4.67]) by list1.zedat.fu-berlin.de (Exim 4.85) for seqan-dev@lists.fu-berlin.de with esmtps (TLSv1.2:DHE-RSA-AES256-GCM-SHA384:256) (envelope-from ) id <1ae4Lg-0030W2-OO>; Thu, 10 Mar 2016 18:26:08 +0100 Received: from infao0809.mpi-klsb.mpg.de ([139.19.1.49] helo=hera.mpi-klsb.mpg.de) by relay1.zedat.fu-berlin.de (Exim 4.85) for seqan-dev@lists.fu-berlin.de with esmtps (TLSv1.2:DHE-RSA-AES128-SHA:128) (envelope-from ) id <1ae4Lg-002Jbm-IL>; Thu, 10 Mar 2016 18:26:08 +0100 DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; d=mpi-inf.mpg.de; 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<8011af3d1a0d43459ca4011dbcc79ad2.squirrel@mail.mpi-inf.mpg.de> In-Reply-To: <7DB8383C-5840-4013-A309-56735F3B98EF@fu-berlin.de> References: <3275efa85bb114a748d59692074cd89f.squirrel@mail.mpi-inf.mpg.de> <1960016.BlySc0OUpc@celegans.imp.fu-berlin.de> <7DB8383C-5840-4013-A309-56735F3B98EF@fu-berlin.de> Date: Thu, 10 Mar 2016 18:26:04 +0100 From: "Luis Enrique Ramirez Chavez" To: "SeqAn Development" User-Agent: SquirrelMail/1.4.23 [SVN] MIME-Version: 1.0 Content-Type: text/plain;charset=utf-8 Content-Transfer-Encoding: 8bit X-Priority: 3 (Normal) Importance: Normal X-MPI-Local-Sender: true X-Originating-IP: 139.19.1.49 X-purgate: suspect X-purgate-type: suspect X-purgate-ID: 151147::1457630768-00052D45-5F34B789/2/19173344301 X-Bogosity: Ham, tests=bogofilter, spamicity=0.029031, version=1.2.4 X-Spam-Flag: NO X-Spam-Status: No, score=-1.4 required=5.0 tests=DKIM_SIGNED,DKIM_VALID, DKIM_VALID_AU,FU_XPURGATE_SUSP,RCVD_IN_DNSWL_MED,RP_MATCHES_RCVD,SPF_PASS X-Spam-Checker-Version: SpamAssassin 3.4.1 on Tokelau.ZEDAT.FU-Berlin.DE X-Spam-Level: Subject: Re: [Seqan-dev] problem in LoadReads X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.16 Precedence: list Reply-To: SeqAn Development List-Id: SeqAn Development List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Thu, 10 Mar 2016 17:26:09 -0000 Hi Temesgen, Thanks for your response typedef seqan::FragmentStore<> THMMFragStore; THMMFragStore fragStore; if (!loadReads(fragStore, fn1_i, fn2_i)){ return false; } The reads are fastq format very small 5 megabytes each. Regards, Luis Ramirez > I tried to reproduce your bug with the following simple code fragment: > > FragmentStore<> store; > > CharString fileNameR = > “~/workspace/example/reads_pe_N6000.GA.R.fastq"; > CharString fileNameL = > “~/workspace/example/reads_pe_N6000.CT.L.fastq"; > > loadReads(store, fileNameR, fileNameR); > > and I couldn’t. All the reads were loaded correctly. > > Can you please provide me with a code fragment that can produce the > problem? > > Thanks! > > Temesgen H. Dadi > PhD Candidate (IMPRS-CBSC, JSMC) > Skype ID: temeehi > Freie Universität Berlin > Institut für Informatik | Institut für > Mikrobiologie > AG Algorithmische Bioinformatik | und > Tierseuche > Takustraße 9, 14195 Berlin, Germany | Robert-von-Ostertag-Str. > 7-13 > Telephone: +49 (0)30 838-75246 | Gebäude 35, 14163 Berlin, > Germany > > > > > >> On 22 Feb 2016, at 12:24, Hannes Hauswedell >> wrote: >> >> Am Montag, 22. Februar 2016, 11:23:23 schrieb Luis Enrique Ramirez >> Chavez: >>> Hi Seqan Devs, >>> >>> I am currently working a project that used Seqan 1.4 and now I am >>> updating >>> to Seqan 2.1. I think that maybe I have found a bug in Seqan. The >>> problem >>> is that LoadReads from FragmentStore is not returning the same as in >>> the >>> previous version for the same call, I did a little research comparing >>> both versions. >> >> Thanks for your bug report and research! >> >>> The code of loadReads have change from one version to the other, in >>> both >>> versions it's defined in seqan/store/store_io.h at line 1159 for old >>> version and at line 1273 for the new version but the behave is >>> different >>> and I think here is the problem. >>> >>> in old version there is this part: >>> >>> MultiSeqFile multiSeqFileL, multiSeqFileR; >>> if (!open(multiSeqFileL.concat, toCString(fileNameL), OPEN_RDONLY)) >>> return false; >>> if (!open(multiSeqFileR.concat, toCString(fileNameR), OPEN_RDONLY)) >>> return false; >> >> This looks like the file is from a previous save() so it is in SeqAn >> binary >> format. >> >> >>> The flow is working correctly and the ifs don't reach the return false >>> but >>> in the new version the code is like this >>> >>> SeqFileIn seqFileL, seqFileR; >>> if (!open(seqFileL, toCString(fileNameL)) || !open(seqFileR, >>> toCString(fileNameR))) >>> return false; >> >> This looks like it is trying to load it as a regular sequence file so >> this >> seems something different from above. You might be right, that this is >> the >> place! >> >>> here the execution always always return false. I inspected and its >>> because >>> a different open function its called and here is where I think is the >>> bug. >>> >>> In seqan 1.4 the open function called is from string_map defined in >>> /include/seqan/file/string_mmap.h however in 2.x the open function that >>> is >>> being called is from /include/seqan/stream/formatted_file.h. The open >>> from >>> string_mmap.h exists in 2.x and I think is the function that wanted to >>> be >>> called. LoadReads calls open with SeqFileIn in the new version while in >>> previous with MultiSeqFile but MultiSeqFile is not available in new >>> version >>> >>> Can you please check if that is a bug >> >> I have created an issue in the bugtracker that you can follow: >> https://github.com/seqan/seqan/issues/1484 >> >> Best regards, >> Hannes >> -- >> Hannes Hauswedell >> >> PhD student >> Max Planck Institute for Molecular Genetics / Freie Universität Berlin >> >> address Institut für Informatik >> Takustraße 9 >> Room 019 >> 14195 Berlin >> telephone +49 (0)30 838-75241 >> fax +49 (0)30 838-75218 >> e-mail hannes.hauswedell@[molgen.mpg.de|fu-berlin.de] >> >> _______________________________________________ >> seqan-dev mailing list >> seqan-dev@lists.fu-berlin.de >> https://lists.fu-berlin.de/listinfo/seqan-dev > > _______________________________________________ > seqan-dev mailing list > seqan-dev@lists.fu-berlin.de > https://lists.fu-berlin.de/listinfo/seqan-dev > From temesgen.dadi@fu-berlin.de Mon Mar 14 10:01:38 2016 Received: from outpost9.zedat.fu-berlin.de ([130.133.4.95]) by list1.zedat.fu-berlin.de (Exim 4.85) for seqan-dev@lists.fu-berlin.de with esmtps (TLSv1.2:DHE-RSA-AES256-GCM-SHA384:256) (envelope-from ) id <1afONe-001y4w-74>; Mon, 14 Mar 2016 10:01:38 +0100 Received: from relay2.zedat.fu-berlin.de ([130.133.4.80]) by outpost.zedat.fu-berlin.de (Exim 4.85) for seqan-dev@lists.fu-berlin.de with esmtps (TLSv1.2:DHE-RSA-AES256-GCM-SHA384:256) (envelope-from ) id <1afONe-003gnJ-1u>; Mon, 14 Mar 2016 10:01:38 +0100 Received: from cas3.campus.fu-berlin.de ([130.133.170.203]) by relay2.zedat.fu-berlin.de (Exim 4.85) for seqan-dev@lists.fu-berlin.de with esmtps (TLSv1:AES256-SHA:256) (envelope-from ) id <1afONd-0023o4-QN>; Mon, 14 Mar 2016 10:01:37 +0100 Received: from EX01B.campus.fu-berlin.de ([130.133.170.131]) by CAS3.campus.fu-berlin.de ([130.133.170.203]) with mapi id 14.03.0279.002; Mon, 14 Mar 2016 10:01:36 +0100 From: "Dadi, Temesgen Hailemariam" To: SeqAn Development Thread-Topic: [Seqan-dev] problem in LoadReads Thread-Index: AQHRbVsijJ7WfTw5JUiTV4U8pf3JIJ8325mAgBgviACAAu09AIAFzSSA Message-ID: References: <3275efa85bb114a748d59692074cd89f.squirrel@mail.mpi-inf.mpg.de> <1960016.BlySc0OUpc@celegans.imp.fu-berlin.de> <7DB8383C-5840-4013-A309-56735F3B98EF@fu-berlin.de> <8011af3d1a0d43459ca4011dbcc79ad2.squirrel@mail.mpi-inf.mpg.de> In-Reply-To: <8011af3d1a0d43459ca4011dbcc79ad2.squirrel@mail.mpi-inf.mpg.de> Accept-Language: en-US, de-DE Content-Language: en-US X-MS-Has-Attach: yes X-MS-TNEF-Correlator: Content-Type: multipart/signed; protocol="application/pkcs7-signature"; micalg=sha256; boundary="B_3540794495_10877303" MIME-Version: 1.0 Date: Mon, 14 Mar 2016 10:01:35 +0100 X-Original-Date: Mon, 14 Mar 2016 09:01:35 +0000 X-Originating-IP: 130.133.170.203 X-Original-X-Originating-IP: [130.133.170.191] X-ZEDAT-Hint: XA X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1457946098-00000D1A-B4C5F9C2/0/0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.000000, version=1.2.4 X-Spam-Flag: NO X-Spam-Status: No, score=-50.0 required=5.0 tests=ALL_TRUSTED,RP_MATCHES_RCVD X-Spam-Checker-Version: SpamAssassin 3.4.1 on Niue.ZEDAT.FU-Berlin.DE X-Spam-Level: Subject: Re: [Seqan-dev] problem in LoadReads X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.16 Precedence: list Reply-To: SeqAn Development List-Id: SeqAn Development List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Mon, 14 Mar 2016 09:01:39 -0000 --B_3540794495_10877303 Content-type: text/plain; charset="ISO-8859-1" Content-transfer-encoding: quoted-printable Hi Luis, That is exactly the same code fragment as mine. What kind of files are fn1_i and fn2_i? Are they fasta/fastq? zipped/compressed? Could you please upload them or attach them so that I could investigate further? Any file producing your problem will work. If not could you please try by assigning fn1_i and fn1_i to the fastq file seqan-src/tests/seq_io/test_dna.fq I suspect the files are either corrupted or contain some invalid fastq records. In SeqAn 2.0 we added a validity check for fastq records and may be that is causing a problem. Thanks, Temesgen On 10/03/16 18:26, "Luis Enrique Ramirez Chavez" wrote: >Hi Temesgen, > >Thanks for your response > >typedef seqan::FragmentStore<> THMMFragStore; > >THMMFragStore fragStore; > >if (!loadReads(fragStore, fn1_i, fn2_i)){ > return false; >} > > >The reads are fastq format very small 5 megabytes each. > >Regards, >Luis Ramirez > > >> I tried to reproduce your bug with the following simple code fragment: >> >> FragmentStore<> store; >> >> CharString fileNameR =3D >> =B3~/workspace/example/reads_pe_N6000.GA.R.fastq"; >> CharString fileNameL =3D >> =B3~/workspace/example/reads_pe_N6000.CT.L.fastq"; >> >> loadReads(store, fileNameR, fileNameR); >> >> and I couldn=B9t. All the reads were loaded correctly. >> >> Can you please provide me with a code fragment that can produce the >> problem? >> >> Thanks! >> >> Temesgen H. Dadi >> PhD Candidate (IMPRS-CBSC, JSMC) >> Skype ID: temeehi >> Freie Universit=E4t Berlin >> Institut f=FCr Informatik | Institut f=FCr >> Mikrobiologie >> AG Algorithmische Bioinformatik | und >> Tierseuche >> Takustra=DFe 9, 14195 Berlin, Germany | Robert-von-Ostertag-Str. >> 7-13 >> Telephone: +49 (0)30 838-75246 | Geb=E4ude 35, 14163 Berlin, >> Germany >> >> >> >> >> >>> On 22 Feb 2016, at 12:24, Hannes Hauswedell >>> wrote: >>> >>> Am Montag, 22. Februar 2016, 11:23:23 schrieb Luis Enrique Ramirez >>> Chavez: >>>> Hi Seqan Devs, >>>> >>>> I am currently working a project that used Seqan 1.4 and now I am >>>> updating >>>> to Seqan 2.1. I think that maybe I have found a bug in Seqan. The >>>> problem >>>> is that LoadReads from FragmentStore is not returning the same as in >>>> the >>>> previous version for the same call, I did a little research comparing >>>> both versions. >>> >>> Thanks for your bug report and research! >>> >>>> The code of loadReads have change from one version to the other, in >>>> both >>>> versions it's defined in seqan/store/store_io.h at line 1159 for old >>>> version and at line 1273 for the new version but the behave is >>>> different >>>> and I think here is the problem. >>>> >>>> in old version there is this part: >>>> >>>> MultiSeqFile multiSeqFileL, multiSeqFileR; >>>> if (!open(multiSeqFileL.concat, toCString(fileNameL), OPEN_RDONLY)) >>>> return false; >>>> if (!open(multiSeqFileR.concat, toCString(fileNameR), OPEN_RDONLY)) >>>> return false; >>> >>> This looks like the file is from a previous save() so it is in SeqAn >>> binary >>> format. >>> >>> >>>> The flow is working correctly and the ifs don't reach the return false >>>> but >>>> in the new version the code is like this >>>> >>>> SeqFileIn seqFileL, seqFileR; >>>> if (!open(seqFileL, toCString(fileNameL)) || !open(seqFileR, >>>> toCString(fileNameR))) >>>> return false; >>> >>> This looks like it is trying to load it as a regular sequence file so >>> this >>> seems something different from above. You might be right, that this is >>> the >>> place! >>> >>>> here the execution always always return false. I inspected and its >>>> because >>>> a different open function its called and here is where I think is the >>>> bug. >>>> >>>> In seqan 1.4 the open function called is from string_map defined in >>>> /include/seqan/file/string_mmap.h however in 2.x the open function >>>>that >>>> is >>>> being called is from /include/seqan/stream/formatted_file.h. The open >>>> from >>>> string_mmap.h exists in 2.x and I think is the function that wanted to >>>> be >>>> called. LoadReads calls open with SeqFileIn in the new version while >>>>in >>>> previous with MultiSeqFile but MultiSeqFile is not available in new >>>> version >>>> >>>> Can you please check if that is a bug >>> >>> I have created an issue in the bugtracker that you can follow: >>> https://github.com/seqan/seqan/issues/1484 >>> >>> Best regards, >>> Hannes >>> -- >>> Hannes Hauswedell >>> >>> PhD student >>> Max Planck Institute for Molecular Genetics / Freie Universit=E4t Berlin >>> >>> address Institut f=FCr Informatik >>> Takustra=DFe 9 >>> Room 019 >>> 14195 Berlin >>> telephone +49 (0)30 838-75241 >>> fax +49 (0)30 838-75218 >>> e-mail hannes.hauswedell@[molgen.mpg.de|fu-berlin.de] >>> >>> _______________________________________________ >>> seqan-dev mailing list >>> seqan-dev@lists.fu-berlin.de >>> https://lists.fu-berlin.de/listinfo/seqan-dev >> >> _______________________________________________ >> seqan-dev mailing list >> seqan-dev@lists.fu-berlin.de >> https://lists.fu-berlin.de/listinfo/seqan-dev >> > >_______________________________________________ >seqan-dev mailing list >seqan-dev@lists.fu-berlin.de >https://lists.fu-berlin.de/listinfo/seqan-dev --B_3540794495_10877303 Content-Type: application/pkcs7-signature; name="smime.p7s" Content-Transfer-Encoding: base64 Content-Disposition: attachment; filename="smime.p7s" MIIWKgYJKoZIhvcNAQcCoIIWGzCCFhcCAQExDzANBglghkgBZQMEAgEFADALBgkqhkiG9w0B BwGgghOWMIIGNzCCBR+gAwIBAgIHGI1YcI8WsTANBgkqhkiG9w0BAQsFADCBtTELMAkGA1UE BhMCREUxDzANBgNVBAgTBkJlcmxpbjEPMA0GA1UEBxMGQmVybGluMSIwIAYDVQQKExlGcmVp ZSBVbml2ZXJzaXRhZXQgQmVybGluMQ4wDAYDVQQLEwVaRURBVDEwMC4GA1UEAxMnRnJlaWUg VW5pdmVyc2l0YWV0IEJlcmxpbiAtIEZVLUNBIC0gRzAxMR4wHAYJKoZIhvcNAQkBFg9jYUBG VS1CZXJsaW4uREUwHhcNMTQxMTIwMTIxMzIxWhcNMTcxMTE5MTIxMzIxWjCBpzELMAkGA1UE BhMCREUxDzANBgNVBAgTBkJlcmxpbjEPMA0GA1UEBxMGQmVybGluMSIwIAYDVQQKExlGcmVp ZSBVbml2ZXJzaXRhZXQgQmVybGluMS4wLAYDVQQLEyVGYWNoYmVyZWljaCBNYXRoZW1hdGlr 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14:07:42 +0100 Received: from cas3.campus.fu-berlin.de ([130.133.170.203]) by relay2.zedat.fu-berlin.de (Exim 4.85) with esmtps (TLSv1:AES256-SHA:256) (envelope-from ) id <1adHMT-001pSo-R1>; Tue, 08 Mar 2016 14:07:41 +0100 Received: from EX02B.campus.fu-berlin.de ([130.133.170.133]) by CAS3.campus.fu-berlin.de ([130.133.170.203]) with mapi id 14.03.0279.002; Tue, 8 Mar 2016 13:50:08 +0100 From: "Reinert, Knut" To: "Kasseckert, Anja" Thread-Topic: SeqAn UGM signup deadline approaches (14.3) Thread-Index: AQHReTkKZjQnFDvKbECNigeq0aiYhQ== Message-ID: <6C5D1F41-AD9F-4C0A-86D5-22903910A10F@fu-berlin.de> Accept-Language: en-US, de-DE Content-Language: en-US X-MS-Has-Attach: yes X-MS-TNEF-Correlator: Content-Type: multipart/signed; boundary="Apple-Mail=_35CFC752-2918-428C-8A71-FDFACD6C6028"; protocol="application/pkcs7-signature"; micalg=sha1 MIME-Version: 1.0 X-Originating-IP: 130.133.170.203 X-Original-X-Originating-IP: [160.45.43.107] X-ZEDAT-Hint: XA X-purgate: suspect X-purgate-type: suspect X-purgate-ID: 151147::1457442468-00052D45-36D03767/1/5005869288 X-Bogosity: Ham, tests=bogofilter, spamicity=0.009547, version=1.2.4 X-Spam-Flag: NO X-Spam-Status: No, score=-49.0 required=5.0 tests=ALL_TRUSTED, FU_XPURGATE_SUSP, HTML_MESSAGE,RP_MATCHES_RCVD X-Spam-Checker-Version: SpamAssassin 3.4.1 on Tuvalu.ZEDAT.FU-Berlin.DE X-Spam-Level: X-Mailman-Approved-At: Wed, 23 Mar 2016 14:53:37 +0100 Subject: [Seqan-dev] SeqAn UGM signup deadline approaches (14.3) X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.16 Precedence: list Reply-To: SeqAn Development List-Id: SeqAn Development List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Date: Tue, 08 Mar 2016 13:07:49 -0000 X-Original-Date: Tue, 08 Mar 2016 13:50:07 +0100 X-List-Received-Date: Tue, 08 Mar 2016 13:07:49 -0000 --Apple-Mail=_35CFC752-2918-428C-8A71-FDFACD6C6028 Content-Type: multipart/alternative; boundary="Apple-Mail=_727B70A1-51FC-4EBE-B0BF-916E465243F9" --Apple-Mail=_727B70A1-51FC-4EBE-B0BF-916E465243F9 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=utf-8 Dear Colleagues and Friends, The SeqAn UGM meeting will take place end of March in Berlin (see = below). Please relate this mail to anyone interested or suitable mailing lists.=20= I hope you or someone from your group can come to Berlin. The deadline for registering is March 14th. For more information (prelim. program) see: https://www.reinert-lab.de/?p=3D304 For signup please use: = https://docs.google.com/forms/d/1-snCFXo81QPYBOOJW58_yjTmkfFeFp5KfsQU3Ew39= ZY/viewform = =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D We are happy to announce the 2016 SeqAn user meeting supported by the = CIBI (Center for integrative Bioinformatics), a member of of the = de.NBI=C2=A0 (German Network for Bioinformatics = infrastructure). The meeting will take place at FU Berlin from March 30th to April 1st = 2016. The SeqAn user meeting is addressing bioinformatics students and = professionals who want to develop efficient applications for NGS = analysis based on an efficient, well-maintained C++ library. In the = meeting you will hear talks from groups who actively use SeqAn in their = daily work, you will here about how some of the SeqAn apps work and how = they were developed, and finally you get hands-on tutorials to get yo = you started with developing your own SeqAn apps and include them into = workflow systems such as KNIME. All the best, Knut ------------------------------------------------ Prof. Dr.-Ing. Knut Reinert =20 Algorithmic Bioinformatics (FUB) & Efficient Algorithms for omics data (MPI Molgen) Phone/Fax : +49 30 838 [75222/475222]=20 Mobile : +49 160 7195754 (GE) Skype : knut.reinert =09 Web : http://www.reinert-lab.de Twitter : @KnutReinert, @SeqAnLib E-Mail : knut.reinert@fu-berlin.de =20 ------------------------------------------------- --Apple-Mail=_727B70A1-51FC-4EBE-B0BF-916E465243F9 Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=us-ascii

Dear Colleagues and Friends,

The SeqAn UGM meeting = will take place end of March in Berlin (see below).

Please relate this mail to anyone interested or suitable = mailing lists. 
I hope you or someone from your group can come = to Berlin.
The = deadline for registering is March = 14th.

For more information (prelim. program) = see:
https://www.reinert-lab.de/?p=3D304

For signup please = use:
https://docs.google.com/forms/d/1-snCFXo81QPYBOOJW58_yjTmkfFeFp= 5KfsQU3Ew39ZY/viewform

=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
We are happy to announce the 2016 SeqAn user meeting supported by the CIBI (Center for integrative = Bioinformatics), a member of  of the de.NBI (German Network for Bioinformatics = infrastructure).

The meeting will = take place at FU Berlin from March 30th to April 1st = 2016. The SeqAn user meeting is addressing bioinformatics = students and professionals who want to develop efficient applications = for NGS analysis based on an efficient, well-maintained C++ library. In = the meeting you will hear talks from groups who actively use SeqAn in = their daily work, you will here about how some of the SeqAn apps work = and how they were developed, and finally you get hands-on tutorials to = get yo you started with developing your own SeqAn apps and include them = into workflow systems such as = KNIME.


All = the best,

Knut



------------------------------------------------
Prof. Dr.-Ing. Knut Reinert   
Algorithmic Bioinformatics (FUB) &
Efficient Algorithms for omics data (MPI Molgen)

Phone/Fax : +49 30 = 838 [75222/475222] 
Mobile = : +49 160 7195754 = (GE)
Skype : = knut.reinert    
Web      : http://www.reinert-lab.de
Twitter = : @KnutReinert, = @SeqAnLib
E-Mail : = knut.reinert@fu-berlin.de          
-------------------------------------------------
<= /div>

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E=Sophos;i="5.24,411,1454972400"; d="scan'208";a="171466684" Received: from prussik.inria.fr (HELO [138.96.204.198]) ([138.96.204.198]) by mail3-relais-sop.national.inria.fr with ESMTP/TLS/DHE-RSA-AES128-SHA; 29 Mar 2016 17:31:55 +0200 Message-ID: <56FA9FEB.6090605@inria.fr> Date: Tue, 29 Mar 2016 17:31:55 +0200 From: Simon Marillet User-Agent: Mozilla/5.0 (X11; Linux x86_64; rv:31.0) Gecko/20100101 Thunderbird/31.7.0 MIME-Version: 1.0 To: seqan-dev@lists.fu-berlin.de Content-Type: text/plain; charset=utf-8; format=flowed Content-Transfer-Encoding: 7bit X-Originating-IP: 192.134.164.104 X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1459265517-00000D1A-70AB2997/0/0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.017382, version=1.2.4 X-Spam-Flag: NO X-Spam-Status: No, score=-6.0 required=5.0 tests=RCVD_IN_DNSWL_HI, RP_MATCHES_RCVD X-Spam-Checker-Version: SpamAssassin 3.4.1 on Tokelau.ZEDAT.FU-Berlin.DE X-Spam-Level: Subject: [Seqan-dev] Amino acid alphabet and scoring matrices: discrepancy with the doc and typo X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.16 Precedence: list Reply-To: SeqAn Development List-Id: SeqAn Development List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Tue, 29 Mar 2016 15:31:58 -0000 Dear Seqan devs, I would like to mention the two following fact to you but I am not sure they really qualify for a bug report: -- First, the amino-acid alphabet size as in the documentation for seqan 2.0 is 27 ("The ValueSize of AminoAcid is 27"), whereas it is 26 in /basic/alphabet_residue.h The reason is that "O" is mentioned in the doc but not included in the source code. -- Second, among the matrices (of size 26x26) in score/score_matrix_data.h, matrix Pam250 has an extra coma at the end of the last row which is likely to trigger a compile error. Best regards, Simon From rene.maerker@fu-berlin.de Tue Mar 29 17:38:50 2016 Received: from outpost9.zedat.fu-berlin.de ([130.133.4.95]) by list1.zedat.fu-berlin.de (Exim 4.85) for seqan-dev@lists.fu-berlin.de with esmtps (TLSv1.2:DHE-RSA-AES256-GCM-SHA384:256) (envelope-from ) id <1akvjF-002rT7-Lc>; Tue, 29 Mar 2016 17:38:49 +0200 Received: from relay2.zedat.fu-berlin.de ([130.133.4.80]) by outpost.zedat.fu-berlin.de (Exim 4.85) for seqan-dev@lists.fu-berlin.de with esmtps (TLSv1.2:DHE-RSA-AES256-GCM-SHA384:256) (envelope-from ) id <1akvjF-000zFS-GB>; Tue, 29 Mar 2016 17:38:49 +0200 Received: from cas3.campus.fu-berlin.de ([130.133.170.203]) by relay2.zedat.fu-berlin.de (Exim 4.85) for seqan-dev@lists.fu-berlin.de with esmtps (TLSv1:AES256-SHA:256) (envelope-from ) id <1akvjF-001cel-6W>; Tue, 29 Mar 2016 17:38:49 +0200 Received: from EX03A.campus.fu-berlin.de ([130.133.170.134]) by CAS3.campus.fu-berlin.de ([130.133.170.203]) with mapi id 14.03.0279.002; Tue, 29 Mar 2016 17:38:48 +0200 From: =?utf-8?B?UmFobiwgUmVuw6k=?= To: SeqAn Development Thread-Topic: [Seqan-dev] Amino acid alphabet and scoring matrices: discrepancy with the doc and typo Thread-Index: AQHRidAnk/1ngjFrKkuo6FjWAltxyp9wbQOA Message-ID: <26B8BDE7-C27E-45BA-8308-75D5988B3A29@fu-berlin.de> References: <56FA9FEB.6090605@inria.fr> In-Reply-To: <56FA9FEB.6090605@inria.fr> Accept-Language: de-DE, en-US Content-Language: en-US X-MS-Has-Attach: X-MS-TNEF-Correlator: Content-Type: multipart/alternative; boundary="_000_26B8BDE7C27E45BA830875D5988B3A29fuberlinde_" MIME-Version: 1.0 Date: Tue, 29 Mar 2016 17:38:46 +0200 X-Original-Date: Tue, 29 Mar 2016 15:38:46 +0000 X-Originating-IP: 130.133.170.203 X-Original-X-Originating-IP: [87.77.61.203] X-ZEDAT-Hint: XA X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1459265929-00000D1A-9307E1A7/0/0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.000072, version=1.2.4 X-Spam-Flag: NO X-Spam-Status: No, score=-51.0 required=5.0 tests=ALL_TRUSTED,HTML_MESSAGE, RP_MATCHES_RCVD X-Spam-Checker-Version: SpamAssassin 3.4.1 on Tuvalu.ZEDAT.FU-Berlin.DE X-Spam-Level: Subject: Re: [Seqan-dev] Amino acid alphabet and scoring matrices: discrepancy with the doc and typo X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.16 Precedence: list Reply-To: SeqAn Development List-Id: SeqAn Development List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Tue, 29 Mar 2016 15:38:51 -0000 --_000_26B8BDE7C27E45BA830875D5988B3A29fuberlinde_ Content-Type: text/plain; charset="utf-8" Content-Transfer-Encoding: base64 SGkgIFNpbW9uLA0KDQp0aGFua3MgZm9yIGZpbmRpbmcgdGhpcy4gQ291bGQgeW91IHBsZWFzZSBv cGVuIGEgbmV3IGlzc3VlIG9uIGh0dHBzOi8vZ2l0aHViLmNvbS9zZXFhbi9zZXFhbi9pc3N1ZXMu DQpXZSB3aWxsIHRoZW4gYXNzaWduIHRoZSBidWcgYW5kIGZpeCBpdC4NCg0KVGhhbmtzIGEgbG90 LA0KDQpSZW7DqSBSYWhuDQoNCk9uIDI5IE1hciAyMDE2LCBhdCAxNzozMSwgU2ltb24gTWFyaWxs ZXQgPHNpbW9uLm1hcmlsbGV0QGlucmlhLmZyPG1haWx0bzpzaW1vbi5tYXJpbGxldEBpbnJpYS5m 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